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We've got a page with a ton of jQuery (approximately 2000 lines) that we want to trim down b/c it is a maintenance nightmare, and it might be easier to maintain on the server. We've thought about using UpdatePanel for this. However, we don't like the fact that the UpdatePanel is sending the whole page back to the server.

Don't move to UpdatePanels. After coming from jQuery, the drop in performance would be untenable. Especially on a page as complex as yours sounds.

If you have 2,000 lines of JavaScript code, the solution is to refactor that code. If you put 2,000 lines of C# code in one file, it would be difficult to maintain too. That would be difficult to manage effectively with any language or tool.

If you're using 3.5 SP1, you can use the ScriptManager's new script combining to separate your JavaScript into multiple files with no penalty. That way, you can logically partition your code just as you would with server side code.